The LMS determined the amino acid sequences of about 650 samples. About 440 of these analyses were for unknown protein or peptides and the remainder were for quality control of synthetic peptides. Most of the unknown sequences determined (about 250) were of endogenous peptides eluted from mouse d and b haplotype class I molecules (LI/NIAID, D. Margulies) and from human HLA-A3, -B44, -B14, -B8 and -A1 molecules (LMS). From these analyses, amino acid residues in peptides requisite for peptide binding to particular class I molecules have been determined. This information has been used to search protein sequence databanks for potential antigenic T cell epitopes that are recognized by cytotoxic T lymphocytes which has important implications for vaccine development. Using such an approach several new antigenic epitopes recognized by cytotoxic T lymphocytes specific for influenza virus proteins and myelin basic protein have been identified. In addition, proteins and peptides from a large variety of other sources have been sequenced by the facility. These include CD22 binding proteins and other B cell specific proteins (Kehrl, LIR); HIV proteins (Theodore, LMM; Dayton, LIR); plasma sialoglycoprotein (spg-120) (Basta, LCI); female specific proteins (Coe, RML); constructs of malaria proteins; (Kaslow, LMR); mouse MHC class II endogenous peptides (Sercarz, UCLA); human MHC class II endogenous peptides (Hammerling, German Cancer Research Center; Koning, University of Leiden, the Netherlands; Lew, Walter and Eliza Hall, Australia) and group B Streptococcal hyaluronidase (Pritchard, Univ. Alabama). A disulfide-linked heterodimeric antigen from human B leukemia cells was detected by radioimmunoprecipitation and Western blot analysis using a monoclonal antibody generated against a cell membrane antigen preparation from human B prolymphocytic leukemia cells and found to define an extracellular epitope of the smaller component (beta chain) of a heterodimeric antigen on human B leukemia cells. The antigen from BALL- 1, a human B leukemia cell line, and fresh (uncultured) B prolymphocytic leukemia cells was found to consist of a 44-49 kDa (alpha chain) and a 36-40 kDa (beta chain) component. Determination of the amino terminal amino acid sequences of the alpha and beta chains unequivocally identified them as the human mb-1 and B29 proteins, respectively. We detected three forms of the mb-1 protein which share an identical amino- terminal sequence and likewise, two forms of the B29 protein. A beta- tubulin-like protein was found to co-purify with the mb-1-B29 antigen and we found that there is a strong amino acid sequence homology between the microtubule-binding domains of certain human microtubule-associated proteins and an intracellular segment of the human mb-1 protein.